Hi Peter,
The questions tell me that maybe you didn't read the readme.pdf file before installing MSM?

The readme file covers installing MSM and the requirement to create a new profile to use with MSM.
(FYI - The readme file can be found in the C:\Mach3\Documentation\MachStdMill directory).
The only way that MSM would overwrite "...all my macros.." is if you used a pre-existing profile for MSM. In that case MSM will replace stock M code scripts with the ones that MSM requires to do the additional functionality MSM supports.
Re M3/M4 specifically, with MSM, you do not edit the M3 or M4 macros (the MSM versions of these Mcodes are are compiled macro)s. Instead, MSM provides hooks to call user scripts as part of the MSM M3/M4 actions. I suggest that you look over section 13 of the MSM user manual for operational differences between MSM and the stock Mach 1024 screen sets to avoid additional surprises. Then you can refer to section 15.9 for how to use the MSM M3/M4/M5 customization hooks.
Dave